barcodes reads for testing?

[nick-youngblut]

Summary

It would be useful to have a test dataset of barcodes reads in order to test the demux functioning of nanopype.

Motivation

We would like to multiplex runs, and it would be helpful to run some test demux'ing with nanopype.

Describe alternatives you've considered

Running guppy_barcoder directly

[PanZiwei]

I am also wondering whether it is possible to provide demultiplexing for post-run barcoding with nanopype.

Also, any idea/tutorial on demultiplexing with Guppy?

[giesselmann]

Hi,
sorry for the late response:
I don't have a barcoded dataset that I can make public available.
The demux funciton of nanopype is based on guppy_barcoder, so results should be exactly the same as running it standalone.

To the second question:
I'm not sure what you mean by post-run barcoding? Guppy is documented within the ONT community forum, if you're familiar with python, you might also want to check the code in rules/demux.smk

Pay

[PanZiwei]

Thanks for the quick response!

For the 2nd question, I think the code of Guppy is not open-source, so can you be a little more specific on the code you mention?

I think you can either do barcoding during the running or do post-run barcoding Guppy (correct me if I am wrong). Do you know whether it is practical to demux the original fast5 files? I think the barcoding step can only be applied on FASTQ files after alignment?

Also, based on the documentyou are using Deepbinner for demultiplexing right? Or actually "The demux function of nanopype is based on guppy_barcoder"?

Thank you so much for your help!

[giesselmann]

Ah I see,
I meant code from nanopype, in the repo in rules/demux.smk you find the usage of guppy_barcoder.
You mean demultiplexing and not barcoding, right? I'm not sure if MinKnow can do it during sequencing, we use it only to record the fast5 and do processing later.
I'm leaving the original fast5 as is and run the demux of our pipeline. All batches and resulting files are grouped by barcode than.
Deepbinner is deprecated, I removed it in v1.2.0 of nanopype and rely only on guppy_barcoder atm.